Oh dear, it's been a while since you've posted this, I am sorry for your wait. :(
This might sound like "Captain Obvious", but have you tried a leather/suede cleaner? Heh heh, yeah, I told you it sounds like Captain Obvious, but I'm thinking that might be your best bet. There should be a way to use a cloth to clean just the areas you want to target, without messing up the rest of the shoe.

Personally, I wear Keens most of the time (since I work outside and they get muddy/cruddy), so mine just get tossed into the washing machine... when I'm not hosing them off. =)

I get my Keens at zappos (dot com). While they are a bit pricey, they are a good deal there, the shipping is beyond excellent, and the customer service is even better than that. The last pair I got, they were in my hands the day after I ordered them, and in the (short) interim, they had sent me 2 emails to notify me that they had processed the order, and then shipped the shoes. Then another email 2 days later to make sure I got them on time and to make sure they were ok. Working in direct customer service myself, I like that kind of personal service and follow-through. I really put these shoes through heck and back, but they take a massive beating from me (I'm harder on the toes of shoes than a bike-riding 10 year old dragging his toes across the concrete!), but when they come out of the wash, they look like brand new. :)